this my first attempt to dock a protein and a ligand (plant saponin) using autodock vina. the screenshot I attached is the molecule after docking. does it look normal? my ligand looks so complex compared to other molecules I saw online. do you think i missed any step preparing my ligand or protein?
It looks to me as if you tried to dock a 2D representation of your ligand instead of a 3D model. Since bonds are assigned based on interatomic distances, you get all these excess bonds, and the sugars appear flat. There may be additional problems, but first try to correct the 3D structure of the ligand before docking (e.g. using Open Babel ( https://open-babel.readthedocs.io/en/latest/3DStructureGen/Overview.html ), if you cannot get an experimental 3D structure of your ligand.
PubChem entries for Saponins generally seem to only provide 2D models, their automatic 3D model generation seems to fail "Conformer generation is disallowed since too many atoms"
Annemarie Honegger Thank you so much for your answer. You are right, I took the 2D structure from pubchem because I couldn't find a 3D structure and then docked it directly with my protein. I later found a 3D structure of my saponin on a website called chemspider so I used it for my docking and my results look better than before :)
That happens when we don't take the precaution to check if the ligand is in 3D before doing the calculation. Any molecule editing software can help you and repeat the docking calculation again.
Santiago Bolivar Avila You are right. it was my first attempt and I missed a lot of steps. this my new complex after making sure both are in 3D. looking better right?
This is perfect, the next step is to verify if the chemical structure meets the common structural characteristics, such as double bonds, carbons with 4 bonds,etc, but it is the correct form. Good luck
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